[Bioperl-l] Scoring an overlap

Florent Angly florent.angly at gmail.com
Mon Sep 24 15:07:35 EDT 2007

I see... Thanks for the replies Chad and Chris. Then I have two more 
1/ Do you know how to get a core dump that could help debug my 
segmentation fault? I have produced dumps of binary C programs before 
with gdb. I have used the Perl debugger for Perl scripts. But how to 
deal with C functions called by Perl?
2/ Is there an easier method to calculate an alignment score in BioPerl 
than using Bio::Tools::dpAlign? I didn't seem to locate something else, 
but who knows...
I have workarounds for quantifying the quality of the overlap, so 
calculating a score is not critical for me (though I believe this would 
be the most accurate/adapted method).

Chris Fields wrote:
> As Chad mentioned it could be a stack issue, but it might be worth 
> filing a bug on.  I will note that bioperl-ext has seen very little 
> use in the last few years, so don't expect it to be fixed unless you 
> can contact the ext module author.
> chris
> On Sep 22, 2007, at 8:41 PM, Florent Angly wrote:
>> Eventually, I gave Bio::Tools::dpAlign a try. I had no luck running it
>> when installing its dependency, bioperl-ext v1.4 or v1.5.1. However all
>> the tests passed when installing the CVS version.
>> So finally, here I am trying to score my alignments. For alignments of 2
>> small sequences, it works, but as soon as the sequences get bigger than
>> a few dozen nucleotides, it crashes:
>> Segmentation fault (core dumped)
>> I did not find any help in the documentation...
>> Can I fix this? Is this a bug?
>> Thanks for your help,
>> Florent
>> Florent Angly wrote:
>>> Hi,
>>> I need to quantify how good some overlaps in contigs are. I have
>>> extracted the alignment of the overlapping region and only need to
>>> score it. I noticed the Bio::Tools::dpAlign has a scoring function.
>>> Is it the right tool for the right tool? Is there anything else?
>>> Thank you,
>>> Florent
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> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign

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